Help:Chemical structure drawing/Accelrys Discovery Studio Visualizer
Accelrys Discovery Studio (DS) Visualizer (ADSV) is a software that is best suited to creating static 3D structures of macromolecules and small molecules. Initial structure generation in Accelrys * Open Accelrys DS Visualizer. * Go to File→Open.... * Open the PDB or SDF file of the 3D molecular structure you are going to create a model of. Remember all 3D models must be created using either crystallography data (including from PDB files) or, if this data is unavailable, using a SDF file provided by PubChem that is then optimized using Avogadro. * Right-click the structure and select Display Style... (or press Ctrl+D). Near the top of the popup window should be four tabs: Atom, Graphics, Lighting, Materials. Do the instructions listed in the Display Style settings table and after this click, "OK" to put these settings into effect. * Right-click the structure and select Color→Background.... Choose a background colour that does not appear in the molecule as this will assist in making the structure transparent later. * Go to Chemistry→Element Properties.... Change the colours of the different elements to this palette http://jmol.sourceforge.net/jscolors/, except with carbon coloured black. * Adjust the molecule's angle and zoom to one's liking such that the greatest degree of detail of the molecule is displayed. * Once everything is to one's liking go to File→Save As... and in the file window that pops under Save as type: select Image Files. After this a popup window should appear prompting you to set the size of the PNG file that will be created of your structure, it is best to set the size to as big as possible, as large PNG files leads to higher-quality (less pixelated) SVG files. Open URL ADSV Screenshot.png Open URL popup box ADSV Screenshot.png Mouse mode ADSV Screenshot.png Element properties ADSV Screenshot.png Background colour changing ADSV Screenshot.png Sidebar ADSV screenshot.png Display style material popup ADSV screenshot.png Display style lighting popup ADSV screenshot.png Display style protein popup ADSV screenshot.png Display style graphic popup ADSV screenshot.png Display style popups ADSV screenshot.png Display settings ADSV screenshot.png Formatting in GIMP # Open GIMP. # Go to File→Open and open the file you created using Accelrys. # If you cannot see the GIMP toolbox, press Ctrl+B # Press Shift+O and click on the background colour you selected earlier in the PNG file you have opened in GIMP. Then press U, right-click and go to Select→Grow. # The 'Grow Selection' window that pops up should be set to 1px automatically, but if not set it to 1px, then click, 'OK'. # Then right-click and go to Colors→Color to Alpha.... Click on the coloured box next to From: and before to alpha. In the colour picking window (see http://health-and-medicine.wikia.com/wiki/File:Colour_picker.png) click the eyedropper. Then click 'OK' to both the colour picking and colour to alpha window. # Then press Shift+O again and repeated step 5. # Press the Delete key. # Go to and press File→Overwrite -file name- where -file name- is replaced by the file's name. Notes Category:Accelrys Discovery Studio Visualizer Category:Chemical structure drawing